This proposal builds a new generation of software that provides fast, reliable information to chemists for combinatorial chemistry, library design, high throughput screening, lead optimization, docking, and scoring. The software will let a lab member easily analyze conformations through direct manipulation with a physically realistic model and discover similarities through fast superposition based on steric and electrostatic fit. The proposal builds fast 2D to 3D conversion of small molecule drawings and databases. The software will allow interactive docking of flexible ligands in flexible receptors. Binding affinity will be measured based on several metrics and visualized through 3D graphics, plots, and spreadsheets. The desktop systems will also be streamlined for high throughput screening and docking of databases. PROPOSED COMMERCIAL APPLICATION: This work builds desktop software for chemists and workstation-based tools for modelers. It will directly produce commercial software for medicinal, organic, and combinatorial chemists. It will develop the foundation for library design, 3D database query, and education products.